Avatar: Most lifeforms on Pandora, including much of the vegetation, have bioluminescent cells. The Na'vi have them as markings that form lines, which according to the background serve as a means of identification. Most plants, along with small animals, have a lot of bioluminescence, with larger animals and trees having less, although everything seems to have at least some.

Up to Eleven in the movie of Life of Pi. Apparently every body of water glows piercing blue at night. Justified as bioluminescent plankton and pelagic worms really are very common on the tropical Pacific.

The aliens in Attack the Block have neon turquoise teeth. And a fur so dark it always appears pitch black, thus the teeth are the only visible trait.

The Big G's dorsal plates traditionally light up before or as he uses his Atomic Breath.

The MUTOs from Godzilla (2014) are black with glowing red markings. Godzilla's dorsal plates begin to light up blue, just like they do in the TOHO films. The new film adds in the plates glowing blue from the tail up, à la Godzilla: The Series.

The Tendu of Amy Thomson's The Color of Distance and Through Alien Eyes communicate through changing patterns on their skins. In the dark, their words glow.

When Liu steps into Rudak's dome in Junction Point, every surface is covered in plant-like life that glows in greens and blues. Whether it's just natural, or the result of bioengineering, has yet to be determined.

In Deception Point, the first clue that the meteorite find is fake is that the hole it's in, supposedly sealed for long ages, turns out to contain glowing (and hence fresh) organisms.

"What Is This Thing Called Love?" by Isaac Asimov has a pair of aliens, who communicate using light, having difficulty understanding human biology including speech (which one of them describes as "a sort of complicated coughing").

In Men at Arms, the narrator at one point explains that dungeons and caves (such as the abandoned sewers the protagonists are currently running through) always have bioluminescent mushrooms, or glowing muck, or just glow in general, so passing heroes can see their way. As the protagonists at the moment consist of a dwarf and a troll, both of whom can see in darkness just fine, the effect is somewhat wasted.

During a brief period of unemployment, Sheldon from The Big Bang Theory mentions trying to engineer some bioluminescent goldfish (specifically to serve as an energy efficient pet/nightlight). It doesn't really come up again after a throw-away gag at the end of the episode, but he was successful in creating at least one.

One of the challenges on Face/Off required contestants to design creatures to be displayed under black light as well as visible, meaning the artists had to paint with colors they couldn't even see.

The Most Extreme had the episode "Night Lights", which was all about finding the most extreme bioluminscent creature. The female angler fish won

In the Tracker pilot, Mel catches a glimpse of Cole glowing, something connected to his Cirronian nature and whatever he was doing in the bedroom at the time. (not *that*!)

Tabletop Games

Dungeons & Dragons: Usually in any dungeon crawl situation, there are caves that have bioluminescent moss or lichen growing on the walls/floors.

The Forest, and the creatures who live there in CreaVures. Interestingly, the bioluminescence on the eponymous CreaVures also serves as a representation of your health (with it fading for a while if you're hit), and sometimes as an indication as to whether an aggressive animal is cowering or not (with theirs fading for a bit).

Everything in Alice: Madness Returns' the Deluded Depths. Even Alice's dress has an angler and glowing dots and stripes.

In Terraria, you can find Blinkroot hidden underground, which does exactly what you'd think it does: Blinks. (Though only when it's blooming.) Also to be noted are tall Glowing Mushrooms, also found underground, and better for healing and potion-making than surface 'shrooms. Quite a number of mooks also glow in the dark.

In Skyrim glowing mushrooms can be found growing in some caves. There is also the nirnroot, a plant which glows and makes a sound. Blackreach is a huge underground area full of enemies, ruins, giant glowing mushrooms and crimson nirnroots (which are like regular nirnroots, but are red instead of green). Especially the Dawnguard add-on is fond of this. Both the fauna and flora of forgotten Valley of ancient Falmer love this trope. Caverns are lit by glowing flowers that retract themselves to their shells and animals have glowing blue stripes on them. Similarities with Avatar definitely coincidental.

In Civilization: Beyond Earth, any late-game Harmony colony will develop technology with lots of glowing blue lines on them. This is also true for the Harmony colony's leader, as they presumably genetically modify themselves.

The monsters of Evolve glow brighter the higher their armor. They come in variety of colors, with Goliath being red, Kraken blue, Wraith a white-ish pink, Behemoth orange, and Gorgon a pale green. For non-monster examples, the blitzleopard and mammoth bird wildlife have this as well.

Subnauticaloves this trope. Just about everything alive other then the player has some kind of bioluminescence, with some exceptions such as the Stalkers.

Starbound: Bioluminescence biomes are full of glowing plants, glowing rocks, glowing critters, and glowing chests that may contain blueprints for glowing furniture. Slime biomes are full of glowing slime pods. Florans like to illuminate their homes with glowing plants that give off a muted green light (because they have a profound fear of fire, being plant beings). The ocean floors are lit with "oshrooms", or ocean mushrooms.

Web Comics

In Homestuck, when Kanaya becomes a rainbow drinker, she begins to glow. Her dancestor, Porrim, also bioluminesces, though she is better able to control it.

The Deep: In one episode, the Nektons encounter a species of giant hermit crabs that glow bright blue.

Real Life

The protein Luciferase and its relatives are the cause of natural bioluminescence, for example in fireflies. It has been put into other creatures to create glowing bacteria, etc.

A more famous but unrelated protein is GFP (abbreviation for "Green Fluorescent Protein"). Its derivatives have been established as common tools for scientific research. It's not true bioluminescence: the protein is merely fluorescent, so it only glows under a light source. GloFish, zebra danios genetically engineered to produce this and similar proteins, are marketed as aquarium fish by invoking this trope in real life.

Ravers and Cybergoths have a liking for glowsticks and clothes that imitate bioluminiscence. While it's definitely running off the Rule of Cool, there's also a functional reason behind it: Supposedly, the glow from these sources have a soothing effect on the mind, reducing the chances for a Bad Trip. Considering that these subcultures have a particular leaning towards psychedelic substances ...

There's also the practical side, in that a dark club is, well, dark, which can make it difficult to see people in general and especially difficult to identify their faces. The faint glow of a glowstick may or may not be enough to illuminate facial features, but if you can remember the combination of colors and kinds of glowing clothing your friends are wearing, you may not need to see them. And if nothing else, it's easier to avoid accidentally slamming into another person if they're glowing.

True to the Life of Pi example, there are bioluminescent plankton that inhabit some waters, and glow when agitated or touched. A real time example can be seen here.

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